The District government Monday filed a $1 million civil lawsuit against D.C. Council member Harry Thomas Jr., accusing the Ward 5 Democrat of using grant money and charitable donations for personal golfing trips, hotel stays and a new sport utility vehicle.

At the same time, federal prosecutors confirmed for the first time that Mr. Thomas also is the focus of an ongoing criminal investigation by the U.S. attorney's office for the District of Columbia.

District Attorney General Irvin B. Nathan said a five-month investigation by his office found that more than $300,000 intended for youth baseball programs and other charitable purposes as part of the 2008 budget was passed through multiple organizations, then to Mr. Thomas for his personal use.

“Those funds are all gone,” Mr. Nathan said of the monies provided by the District government and private donors. “We don’t know where they are, but we want them back for the city.”

Mr. Thomas, who represents much of the city’s Northeast area, refuted the attorney general’s allegations at an afternoon news conference.

“Allegations are allegations, fact is fact,” he told reporters outside the John A. Wilson Building.

The suit is the most recent setback for a city council whose reputation has been marred by allegations and investigations related to the misuse of public funds.

A council committee is looking into potential nepotism and questionable hiring practices by the administration of Mayor Vincent C. Gray, a Democrat.

Council Chairman Kwame Brown received two luxury Lincoln Navigators, leased with taxpayer money, after rejecting the first because he didn’t like the color of the interior. And the D.C. Office of Campaign Finance is investigating Council member Yvette Alexander, Ward 7 Democrat, for her questionable use of constituent service funds.

Mr. Thomas said he will fight for his legacy, refuse any settlement offer that suggests he did anything wrong, and would not resign his council seat or the chairmanship of the Council’s Committee on Economic Development.

Mr. Thomas, re-elected last year to a second term, has come under scrutiny largely over Team Thomas, a nonprofit he co-founded in 2000. The organization purportedly ran children’s sports programs until it was dissolved last December.

The attorney general’s office said more than $300,000 in grant funds went to Langston 21st Century Foundation, a purported youth sports and education nonprofit, which is suspected of secretly giving most of the funds to Mr. Thomas through his nonprofit and for-profit organizations. Official documents identify the foundation principles as James Garvin and Marshall Banks.

The attorney general’s office said Mr. Thomas also is accused of soliciting more than $80,000 from private donors on behalf of Team Thomas, which was never registered in the city to do so, and used a Team Thomas debit card to spend more than $20,000 on personal travel and entertainment use — including $1,185 and $1,073 for respective golf trips to Las Vegas and Pebble Beach, Calif.

The office also accused the council member of writing thousands of dollars in checks from the nonprofit’s bank account to himself, his for-profit company, HLT Development, or to “cash” and using $58,000 in funds to buy an Audi Quattro sport utility vehicle, which is registered in his name.

“I have to say we’re extremely disappointed in this violation of public by Mr. Thomas,” Mr. Nathan said, adding he has referred the case to federal investigators.

According to court records, the District funds were provided by Council legislation in 2007 to the D.C. Children & Youth Investment Trust Corp., which at Mr. Thomas‘ direction, passed them to the Langston 21st Century Foundation, which in turn, at Mr. Thomas‘ direction, secretly paid most of the money to Mr. Thomas through his for-profit and non-profit corporations.

Mr. Thomas‘ attorney, Frederick Cooke Jr., said he and his client would not field questions about specific allegations in the lawsuit. He said they received the complaint early Monday and would like to preserve their legal rights.

Still, Mr. Cooke said: “We don’t believe any of these allegations are true.”

Mr. Cooke added that the Audi was purchased through Mr. Thomas‘ for-profit business, and allegations surrounding itemized trips were based on the attorney general’s “view of the business,” and “not ours.”

Mr. Nathan’s announcement of the lawsuit was followed by the U.S. Attorney's Office for the District of Columbia acknowledging publicly in a brief statement that the agency also has been investigating the council member.

“The U.S. Attorney's Office had been investigating the matter prior to today’s development,” spokesman Bill Miller said, although he declined to say when the federal probe started.

The more than $1 million prosecutors are seeking includes penalties and lawyer fees.